Constraining flood fill to size brushsize

Yesterday I came across this video ( from the people of Itkgray ( It’s a branch of ItkSnap.

Here you see them using the paintbrush with a ‘Floodfill’ setting for segmenting the white matter of the brain.

  • Set the active drawing label to ‘white’ with the correct hemisphere.
  • Use the Paintbrush tool to fill in most of the white matter and the ventricles.
    The axial view works well for this; using Floodfill with the 3D brush on at a tolerance of ~5 and/or the square and round brush.
  • It may help to start dorsally and work down, cleaning up the subcortical areas as you progress.

I was wondering if this option is also available in Slicer? I haven’t found it (yet) and from what I noticed, it now only works on the entire 3D-image and you can’t contain it to only a brushsize or other volume.

Or is there maybe a workaround for this? My idea would be to do a coarse, completely filled segmentation with for instance the ‘Fill between slices’ option and then use the ‘Flood filling’, constrained to the coarse segmentation.

Any other suggestions?

You are very lucky. @Sunderlandkyl have just added yesterday (rev 28613) a new effect “Local threshold” Segment Editor effect (via SegmentEditorExtraEffects extension) that does this. It computes an intensity range from a small region that you draw on the image, then you Ctrl-click at the position you want to fill around. You can choose between various fill strategies (flood fill, grow from seeds, watershed) and it works quite robustly in 3D.

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Great work! Lucky me!